The Davao City police reported that the incident occurred at a night market along Roxas Street around 10:30 p.m.
President Duterte was already in Davao City for his usual weekend break and had earlier given a televised news conference in the city.
But Duterte's son Paolo, vice mayor of Davao City, said his father was far from the blast location when the explosion took place.
The explosion was outside a hotel where Duterte visits frequently. He earlier shrugged off rumors of a plot to assassinate him, saying such threats were to be expected.
It was not clear if the explosion was caused by a bomb as earlier reports indicated that a liquify petroleum gas tank may have went off along the busy night market.
President Duterte, in his campaign against drugs, was subjected to series of assassination threats.
The newly-elected president, merely two months in office, gained popularity in his war against drugs, tagging high ranking government officials such as a senator, court judges, police generals, governors and mayors in illegal drug activities.
The numbers of drug-related killings reached 2,000 with most fatalities reportedly engaged in gunfights against authorities while others were believed to be executed by vigilantes.
On Monday, Philippine authorities seized caches of weapon parts that accordingly will be used for the assassination of the President.
Threats further intensify as Duterte embarked in a massive campaign against the ISIS-linked Abu Sayyaf Group in southern Philippines, vowing to finish the terrorist group in months' time.
